From nobody Wed Jun 14 21:23:38 2023 X-Original-To: dev-commits-ports-all@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4QhJLy6c32z4dkRj; Wed, 14 Jun 2023 21:23:38 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4QhJLy67Tdz4FxM; Wed, 14 Jun 2023 21:23:38 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1686777818; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=QcROxy3pNBHlDRKez4gmJXiBKwE9+yvZaxorb/Du/b4=; b=A1YhPVH4+yFLq8If1mTGndT2w61/imTpJnXbhR7R9HOxLurz6rbvJwbbqx2hipFiPpK7DN Enk5/MeY9MxYowrpf7nFxoa5RBX+5K5pFCCMe7suN0GGn3BvPRvslIvne21COJxb7yKkvK cIa5yWoVgps7U35PPxTAZWth30x5MOJzAap13ReCyDr9p72IaAvZ8/R6YFdzez0Y1RsIvH NAnizKPBINit2Y2X4EV9rIKqVJpjyUJelU7NRzcBaJWIDw1RWq/RZ4LuZuzEV+Tf4RRwts meZo0J8s0++kYzamkHrmfy58qZo9heFSN7v7W6m2HR1Tmy/k15JRgCbLYNtKcw== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1686777818; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=QcROxy3pNBHlDRKez4gmJXiBKwE9+yvZaxorb/Du/b4=; b=A4zDoKwvqC3dWG2kmZ4DB3TK6bE6mQmJQJrw/ee81zbc2rYhsq9h0IpyACbWT4e97+D96i y4XCRGK8bbzFgPsvR4V+aiecnR4n5L3bocM+Te5yb5vMXBc5qpFN+ySfL6m/pNf9GQI4qD i9Q6CxNWPJ48t5hCZD8fvWEyiIyvwbVFqTZDGDmeMSzyW9g8kUYUf+E2exN5junJ3a5yUG xXxxbBgnQJYrJ1q6Wsd6Yy+QXYo6hD8PNs7/0/m7Fmk7kFKqn7Qv9ySQ6owrZp/REcgeKT qr4JP2TeJQ6h2O7bnEVnS2T3Ljpu2OusT1/3QtPJYF2aK78UZZla5PPL0vICAA== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1686777818; a=rsa-sha256; cv=none; b=Sj+cNksJ5A6Bn6Ywp3HuATP/xupomKFmMm+Xfo2Kk1ESNsZWpAeRYyUv5yUUw/UfTYO2eX EBseVeo2cOvx05CasVDrIUiRsTZdUAX4KDhD1jOX4yhj4zp0TsqBoa6hVxcaXTmRf/zQlB dZke2yzLR7gVUU/kVCmxUvro5nobQnyZb3eG/QqvoevKf4ft9c8DhXGkW0RGT80YKGI5t2 TaqksKJ1f/xHfo34MRB1ibxuchFARnTbVHcUbCdKWzsLoLFCYWtsoRDCsC+d/62JnRcBI4 3IppaWUlvWNVMISW9WVNTnJ9zZSyq2DD21Zes/+pt4pDAjJu84yTardD/JTDxg== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4QhJLy4t9RzKgW; Wed, 14 Jun 2023 21:23:38 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 35ELNc0v090612; Wed, 14 Jun 2023 21:23:38 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 35ELNccN090611; Wed, 14 Jun 2023 21:23:38 GMT (envelope-from git) Date: Wed, 14 Jun 2023 21:23:38 GMT Message-Id: <202306142123.35ELNccN090611@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: fddb1ea643a5 - main - biology/chip-seq: Metaport for ChIP-Seq analysis List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: fddb1ea643a59874932554e27ec62432a65aa136 Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=fddb1ea643a59874932554e27ec62432a65aa136 commit fddb1ea643a59874932554e27ec62432a65aa136 Author: Jason W. Bacon AuthorDate: 2023-06-14 21:22:35 +0000 Commit: Jason W. Bacon CommitDate: 2023-06-14 21:23:37 +0000 biology/chip-seq: Metaport for ChIP-Seq analysis Metaport to install tools for typical ChIP-Seq analysis, including QC, adapter trimming, alignment, and differential analysis. Presently identical to biology/atac-seq, but may diverge in the future. --- biology/Makefile | 1 + biology/chip-seq/Makefile | 27 +++++++++++++++++++++++++++ biology/chip-seq/distinfo | 1 + biology/chip-seq/pkg-descr | 2 ++ 4 files changed, 31 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 927e88c08f00..c8654fab2077 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -32,6 +32,7 @@ SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += checkm + SUBDIR += chip-seq SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += cufflinks diff --git a/biology/chip-seq/Makefile b/biology/chip-seq/Makefile new file mode 100644 index 000000000000..5714a40951dd --- /dev/null +++ b/biology/chip-seq/Makefile @@ -0,0 +1,27 @@ +PORTNAME= chip-seq +DISTVERSION= 0.1.2 +CATEGORIES= biology python +MASTER_SITES= # empty + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Metaport for ChIP-Seq analysis +WWW= https://github.com/auerlab/ + +LICENSE= BSD2CLAUSE + +RUN_DEPENDS= sra-tools>0:biology/sra-tools \ + fastq-trim>0:biology/fastq-trim \ + fastqc>0:biology/fastqc \ + ${PYTHON_PKGNAMEPREFIX}multiqc>0:biology/py-multiqc@${PY_FLAVOR} \ + biolibc-tools>0:biology/biolibc-tools \ + bwa>0:biology/bwa \ + bowtie2>0:biology/bowtie2 \ + samtools>0:biology/samtools \ + ${PYTHON_PKGNAMEPREFIX}macs2>0:biology/py-macs2@${PY_FLAVOR} \ + fasda>0:biology/fasda \ + peak-classifier>0:biology/peak-classifier \ + webbrowser>0:www/webbrowser + +USES= metaport python + +.include diff --git a/biology/chip-seq/distinfo b/biology/chip-seq/distinfo new file mode 100644 index 000000000000..5912638d4af3 --- /dev/null +++ b/biology/chip-seq/distinfo @@ -0,0 +1 @@ +TIMESTAMP = 1686777697 diff --git a/biology/chip-seq/pkg-descr b/biology/chip-seq/pkg-descr new file mode 100644 index 000000000000..d0bdf18d2c71 --- /dev/null +++ b/biology/chip-seq/pkg-descr @@ -0,0 +1,2 @@ +Metaport to install tools for typical ChIP-Seq analysis, including QC, +adapter trimming, alignment, and differential analysis.